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Unified Genotyper command

ImbeaudImbeaud Paris (FranceMember

Hi,

I am using the unifiedgenotyper tools for variant calling and get as output the follong format

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ARL-MPM-40-lib23_S8

chr1 27107650 . TA T 643.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=250;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.935;QD=2.57;RPA=18,17;RU=A;ReadPosRankSum=-0.375;STR GT:AD:DP:GQ:PL 0/1:155,94:250:99:773,0,2730

However, I would like to get not only GT:AD:DP:GQ:PL but GT:AD:DP:GQ:PL:MQ:GQX:VF.
My command line is the following (see beow). Which option should I add to get additionnal :MQ:GQX:VF info?

java -Xmx64g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R /mnt/MD1200/DATASETS/MISEQ/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFASTA/genome.fa -I ${resultpath}/${foldername}/${i}/${i}_recal.bam -o ${resultpath}/${foldername}/${i}/${i}_UG_variant.calling.vcf -stand_call_conf 1 -stand_emit_conf 30 -glm BOTH -A Coverage -L /mnt/MD1200/DATASETS/MISEQ/panel1meso/fichiers_utils/Amplicon-Interval-List/amplicons-Panel1Meso.intervals

In addition, the same is for HaplotypeCaller tools... Is there a way to get the MQ:GQX:VF info in the vcf file?

Many thanks
/ Sandrine Imbeaud

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